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root/OpenMD/branches/development/src/parallel/ForceMatrixDecomposition.cpp
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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC vs.
Revision 1798 by gezelter, Thu Sep 13 14:10:11 2012 UTC

# Line 557 | Line 557 | namespace OpenMD {
557             atomRowData.electricField.end(), V3Zero);
558        fill(atomColData.electricField.begin(),
559             atomColData.electricField.end(), V3Zero);
560 –    }
561 –
562 –    if (storageLayout_ & DataStorage::dslFlucQForce) {    
563 –      fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
564 –           0.0);
565 –      fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
566 –           0.0);
560      }
561  
562   #endif
# Line 639 | Line 632 | namespace OpenMD {
632        AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
633                                     atomColData.aMat);
634      }
635 <    
636 <    // if needed, gather the atomic eletrostatic frames
637 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
638 <      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
639 <                                atomRowData.electroFrame);
640 <      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
641 <                                   atomColData.electroFrame);
635 >
636 >    // if needed, gather the atomic eletrostatic information
637 >    if (storageLayout_ & DataStorage::dslDipole) {
638 >      AtomPlanVectorRow->gather(snap_->atomData.dipole,
639 >                                atomRowData.dipole);
640 >      AtomPlanVectorColumn->gather(snap_->atomData.dipole,
641 >                                   atomColData.dipole);
642      }
643  
644 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
645 +      AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
646 +                                atomRowData.quadrupole);
647 +      AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
648 +                                   atomColData.quadrupole);
649 +    }
650 +        
651      // if needed, gather the atomic fluctuating charge values
652      if (storageLayout_ & DataStorage::dslFlucQPosition) {
653        AtomPlanRealRow->gather(snap_->atomData.flucQPos,
# Line 1042 | Line 1042 | namespace OpenMD {
1042     * the parallel decomposition.
1043     */
1044    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1045 <    int unique_id_1, unique_id_2, group1, group2;
1045 >    int unique_id_1, unique_id_2;
1046          
1047   #ifdef IS_MPI
1048      // in MPI, we have to look up the unique IDs for each atom
1049      unique_id_1 = AtomRowToGlobal[atom1];
1050      unique_id_2 = AtomColToGlobal[atom2];
1051 <    group1 = cgRowToGlobal[cg1];
1052 <    group2 = cgColToGlobal[cg2];
1051 >    // group1 = cgRowToGlobal[cg1];
1052 >    // group2 = cgColToGlobal[cg2];
1053   #else
1054      unique_id_1 = AtomLocalToGlobal[atom1];
1055      unique_id_2 = AtomLocalToGlobal[atom2];
1056 <    group1 = cgLocalToGlobal[cg1];
1057 <    group2 = cgLocalToGlobal[cg2];
1056 >    int group1 = cgLocalToGlobal[cg1];
1057 >    int group2 = cgLocalToGlobal[cg2];
1058   #endif  
1059  
1060      if (unique_id_1 == unique_id_2) return true;
# Line 1132 | Line 1132 | namespace OpenMD {
1132        idat.A2 = &(atomColData.aMat[atom2]);
1133      }
1134      
1135 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
1136 <      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1137 <      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1138 <    }
1139 <
1140 <    if (storageLayout_ & DataStorage::dslTorque) {
1135 >    if (storageLayout_ & DataStorage::dslTorque) {
1136        idat.t1 = &(atomRowData.torque[atom1]);
1137        idat.t2 = &(atomColData.torque[atom2]);
1138      }
1139  
1140 +    if (storageLayout_ & DataStorage::dslDipole) {
1141 +      idat.dipole1 = &(atomRowData.dipole[atom1]);
1142 +      idat.dipole2 = &(atomColData.dipole[atom2]);
1143 +    }
1144 +
1145 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1146 +      idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1147 +      idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1148 +    }
1149 +
1150      if (storageLayout_ & DataStorage::dslDensity) {
1151        idat.rho1 = &(atomRowData.density[atom1]);
1152        idat.rho2 = &(atomColData.density[atom2]);
# Line 1181 | Line 1186 | namespace OpenMD {
1186        idat.A2 = &(snap_->atomData.aMat[atom2]);
1187      }
1188  
1184 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1185 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1186 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1187 –    }
1188 –
1189      if (storageLayout_ & DataStorage::dslTorque) {
1190        idat.t1 = &(snap_->atomData.torque[atom1]);
1191        idat.t2 = &(snap_->atomData.torque[atom2]);
1192 +    }
1193 +
1194 +    if (storageLayout_ & DataStorage::dslDipole) {
1195 +      idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1196 +      idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1197      }
1198  
1199 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1200 +      idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1201 +      idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1202 +    }
1203 +
1204      if (storageLayout_ & DataStorage::dslDensity) {    
1205        idat.rho1 = &(snap_->atomData.density[atom1]);
1206        idat.rho2 = &(snap_->atomData.density[atom2]);
# Line 1339 | Line 1349 | namespace OpenMD {
1349          for (int j = 0; j < 3; j++) {
1350            scaled[j] -= roundMe(scaled[j]);
1351            scaled[j] += 0.5;
1352 +          // Handle the special case when an object is exactly on the
1353 +          // boundary (a scaled coordinate of 1.0 is the same as
1354 +          // scaled coordinate of 0.0)
1355 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1356          }
1357          
1358          // find xyz-indices of cell that cutoffGroup is in.
# Line 1363 | Line 1377 | namespace OpenMD {
1377          for (int j = 0; j < 3; j++) {
1378            scaled[j] -= roundMe(scaled[j]);
1379            scaled[j] += 0.5;
1380 +          // Handle the special case when an object is exactly on the
1381 +          // boundary (a scaled coordinate of 1.0 is the same as
1382 +          // scaled coordinate of 0.0)
1383 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1384          }
1385          
1386          // find xyz-indices of cell that cutoffGroup is in.
# Line 1389 | Line 1407 | namespace OpenMD {
1407          for (int j = 0; j < 3; j++) {
1408            scaled[j] -= roundMe(scaled[j]);
1409            scaled[j] += 0.5;
1410 +          // Handle the special case when an object is exactly on the
1411 +          // boundary (a scaled coordinate of 1.0 is the same as
1412 +          // scaled coordinate of 0.0)
1413 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1414          }
1415          
1416          // find xyz-indices of cell that cutoffGroup is in.

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